(092112)

Biochemical Molecular Machines Cellular Design

Questions:

Can we magnify life to see splendid machinery at work?

Has humanity
become so use to modern technologies that we fail to see the awesome and
splendid intricacies of life's systems? And what does this machinery tell
us?

What
context or unique perspective can help us to see living cells as more than
evolution's end product?

How might some
quality, structure, function, or characteristic reveal that the cell is
much more than simply a smaller component of a plant or animal's body?

Scientists
today routinely report the incredible structural detail and the inner imperceptible
functions of chemicals that give life a flow and productive character. How can we hope to capture the larger dimension of what is revealed from
within all the detail?

Short Answer:

If
you can visualize a living cell's life systems in terms of a factory,
production lines, processes directed by information, all working at
maximum capacity and top speed ... then life becomes redefined in an
entirely remarkable context. How could something called life appear so well coordinated and designed?

Only
with the discovery of the molecular basis of life has science
been able to address questions about life's basic mechanisms.
Science has learned over the past four decades that the many cellular
tasks required to sustain life are carried out by machines—literally,
molecular machines. Behe (MC) Page 177

The WindowView
now enlarges cell details to think with a bit of wonder about
all the ultra-structures and inner workings of life. Take a really close
look at the finer scale to life and to dimensions that make what's really
small to have really huge implications! Every cell in your body exhibits
something incredibly well designed ... now multiply that by the number
of cells inside of you!

We are not
talking about coordinating systems on any small scale. The number of
cells in one organism speak to the number of places where a complete
library of genetic information is stored. This number is also indicative
of the number of compartments that are interlinked and structure into
tissues and thereafter into organs that function in a specific set of
high order tasks to keep the larger organisms on track, functioning,
and alive to the next generation. Meanwhile, each little compartment
is a veritable array of functions and a master work in its own right.

The
machinelike parts and coordination of chemical production within
cells requires a discerning look. Blow up the cell, crawl inside,
take a close look ... then it becomes clear
that these structures are wonderful and so far beyond a chance
construction that evolution falls far short of explaining what
we see. But, indeed, do take that look. With just a bit
of imagination helps in visualizing what this is all about ...
then you can see that many who study these cellular structures
have missed how extraordinary life truly is.

Consider This:

From the dawn of light
microscopy's first glimpse into life, science had a general appreciation for
the presence of cells within living forms. In the 1600's light microscopes
were greatly enhanced by better lenses and greater magnifying power. But at
no time in all of human history was there ever a greater biological epiphany
than when electron microscopes began to reveal the incredible intricacy within
cells—from single celled organisms to cells in complex beings such as
in our own human bodies. In fact, it seems incredible that anyone looking
at the diagrams in a scientific weekly—such as Science or Nature—wouldn't
readily agree that cellular structures and associated biochemical pathways
are phenomenally organized and intricate. Every aspect of these publications'
illustrations suggests a sculpting and design on the smallest scale—functional
components working at the smallest of all possible levels.

Protein
molecules are the ultimate stuff of life. If we think of the cell
as being analogous to a factory, then the proteins can be thought
of as analogous to the machines on the factory floor which carry out
individually or in groups of all the essential activities on which
the life of the cell depends. Each protein is a sort of micro-miniaturized
machine, so small that it must be magnified a million times before
it is visible to the human eye. The structure and functioning of these
fascinating work horses of the cell was a complete mystery until the
1950s. Denton (ETC) Page
234

Each
enzyme is a single large protein molecule consisting of some several
thousand atoms linked together to form a particular spatial configuration
which confers upon the molecule the capacity to carry out a unique
chemical operation. Denton
(ETC) Page 334

But faced with what
seems the entirely inconceivable, scientists treat such detail as a fact
of the ordinary—but with a moment's deeper reflection—reveals
the small cellular details take on immense meaning. They are not ordinary.
They are entirely mechanical, but are well tailored to specific jobs, and
perhaps engineered beyond the reach of evolutionary natural selection and
the supposed gradualism that is implied to be the pathway of decent from ancestral
life forms. In fact what we call primitive cells embody complexities that
are found in the cells of more complex organisms.

Molecular
biology has shown that even the simplest of all living systems on the
earth today, bacterial cells, are exceedingly complex objects. Although
the tiniest bacterial cells are incredibly small, weighing less than 10-12 gms, each is in effect a veritable micro-miniaturized factory containing
thousands of exquisitely designed pieces of intricate molecular machinery,
made up altogether of one hundred thousand million atoms, far more complicated
than any machine built by man and absolutely without parallel in the nonliving
world.
Denton (ETC) Page 250

The complexity of life
is routinely paraded across the pages and illustrations of technical weeklies
entitled 'Science' and 'Nature.' Other periodicals—'Time,' 'Newsweek,'
'Scientific American,' et al. —make the same topics more approachable
by wider audiences. Yet a basic appreciation for what we all see is lost in
the technical descriptions. First, life is very complex and second explaining
the level of complexity we now observe is no simple matter ... it begs questions
concerning origin, design, and precision that exceeds chance. Could primitive
forms of molecules easily lead to the more advanced?

The
impossibility of gradual functional transformation is virtually self-evident
in the case of proteins:
mere causal observation reveals that a protein is an interacting whole,
the function of every amino acid being more or less (like letters
in a sentence or cogwheels is in a watch) essential to the function
of the entire system. Denton
(ETC) Page 321

How would one track evolution
of molecules to the current working protein in a cell? The remarkable shape
and specific site of activity on a protein (e.g., enzyme) doesn't allow much
room for scenarios where a lineage of nonfunctional proteins would precede
the functional entity. How does a life form function based on an array of
nonfunctional components. That's like saying a sentence or meaning existed
near it's origin with gibberish in place of intelligible language. When does
the gibberish turn into fully functional words? Can a meaningful sentence
exist as gibberish until the words are properly set in place? Can production
of non-functional protein be sustained while it is transformed to its fully
evolved state?

But amino acids in a protein
are not the same as moving letters or words around! Moving amino acids into
and out of a protein changes the entire scheme of bonds, the overall shape
of the molecule, and thus destabilizing the molecule to the point of being
useless. Meanwhile, proteins as enzymes do not work
alone. In this regard a coordinated series of changes would be required to
make life possible.

Life's Machines, the Details

We've included a diagram
of a cell as it appears in a 1924 biology textbook (diagram A). This is about as much detail
as Darwin could see in a light microscope available to him in his day. A living
cell might display inner streaming motion, but the detail within revealed
nothing more than randomness, globules, particles, or variations in indistinct
shape and color.

With the advent of
electron microscopes and more sophisticated light microscopy, the cell takes
on an entirely different appearance. We can now magnify the cellular details
a thousand million times ...

... until it is twenty kilometers in diameter
and resembles a giant airship large enough to cover a great city like
London or New York. What we would then see would be an object of unparalleled
complexity and adaptive design. Denton
(ETC) Page 328

Look to the right of
the (Fig 3.) "Diagram of a cell" (diagram A) below and you'll find an image from an electron microscope (diagram B). This photo is not magnified nearly
as much as an electron microscope can do. But look at the line drawing of
the membrane below this photo image (diagram C).
The two layers of molecules that make up the membrane sheet and the large
protein or carbohydrate molecules that extend into or across the membrane
are our current refined view of life's highly ordered appearance.

Give those molecules
all their specific jobs and add the rates of speed at which they service the
cell or tissues around them and this static picture just zooms with activity
and remarkable efficiency. Darwin and science—until shortly after World
War II—had no clue of life at the molecular level.

A: An artist's representation (above) of the cell from the turn of the
Twentieth Century. The amount of detail is limited, much like what
was available to scientists to scrutinize in Darwin's day.

B: An electron microscope (EM) image form a plant cell—many thousands
of times beyond the magnification made possible by a light microscope.

C: Electron microscopy, along with advances in biochemical research, now
makes it possible to understand a membrane of a cell, its structure
down to single molecular components, and the function of each type of
molecule.

However, take the images
and science data that accompany the structural and functional aspects to what
we see and add a bit of poetic license AND the whole picture consumes our
imagination to describe a reality that is way beyond our daily perception.
But this describes the inner workings of our material being. Let's take a
look as Dr. Denton moves from the outer membrane of a cell to the inner parts
of this compartment of life.

On
the surface of the cell we would see millions of openings, like the
portholes of a vast space ship, opening and closing to allow a continual
stream of materials to flow in and out. If we were to enter one of these
openings with find ourselves in a world of supreme technology and bewildering
complexity. We would see endless highly organized corridors and conduits
branching in every direction away from the perimeter of the cell, some
leading to the central memory bank in the nucleus and others to assembly
plants and processing units. The nucleus of itself would be a vast spherical
chamber more than a kilometer in diameter, resembling a geodesic dome
inside of which we would see, all neatly stacked together in ordered
arrays, the miles of coiled chains of the DNA molecules. A huge range
of products and raw materials would shuttle along all the manifold conduits
in a highly ordered fashion to and from all the various assembly plants
in the outer regions of the cell. Denton (ETC) Page 328

Proteins are key mechanical
components in life. They are like the cell's engineered automatons—specific
tooled machines—displaying astonishing complexity based on thousands
of atoms that uniquely make specific functional three-dimensional configurations.

When a number
of enzymes are necessary for the assembly of a particular compound,
they are arranged adjacent to each other so that, after each step in
the operation, the partially completed compound can be conveniently
passed to the next enzyme which performs the next chemical operation
and so on until the compound is finally assembled. The process is so
efficient that some compounds can be assembled in less than a second,
while in many cases the same synthetic operations carried out by chemists,
even in a well-equipped lab, would take several hours or days or even
weeks. Denton (ETC) Page 334

The cell, however,
manufactures all its component structures, even the most complex,
by fully automated assembly techniques which are perfectly regulated
and controlled. Unlike our own a pseudo-automated assembly plants,
where external controls are being continually applied, the cell's
manufacturing capacity is entirely self-regulated. Denton
(ETC) Page 335

Whoa ... hold on tight
... not only is the machinery intricate, the efficiency of the way these molecules
work is at WARP speed. What goes on at the cell level can be mimicked but
not be reproduced in a modern laboratory. And there is the sense that all
this is directed. So, beyond the physical presence of all the cell components
is the issue of the information that drives all processes to sustain life
at all levels.

We
would see that nearly every feature of our own advanced machines had
its analogue in the cell: artificial languages and their decoding
systems, memory banks for information storage and retrieval, elegant
control systems regulating the automated assembly of parts and components,
error fail-safe and proof-reading devices
utilized for quality control, assembly processes involving the principle
of pre-fabrication and modular construction. In fact, so deep would
be the feeling of deja-vu, so persuasive the analogy, that
much of the terminology we would use to describe this fascinating
molecular reality would be borrowed from the world of late twentieth-century
technology. Denton
(ETC) Page 329

We can think of the
cell as a marvelous factory, full of activity, speed, efficiency, and modular
sub-unit of tissues and organs in the body. But there is one more remarkable
feature that exceeds the likes of a typical factory. The cell is able to completely
replicate itself within a matter of hours. What
machine or factory is capable of that! The cell, as a factory,
surpasses anything engineered by human material production platforms.

LET'S
MAKE A MODEL!

Dr. Denton suggests we think in terms of constructing
an atomic model of the cell. Take one atom at a time and simply put it into
the model. How long would it take to build the model?

A typical cell contains some ten million million atoms.

Suppose we chose to build an exact replica to a scale of one thousand
million times that of the cell so that each atom of the model would
be the size of a tennis ball. Constructing such a model at the rate
of one atom per minute, it would take fifty million years to finish,
and the object we would end up with would be the giant factory, described
above, some twenty kilometers in diameter, with a volume thousands of
times that of the Great Pyramid. Denton
(ETC) Page 330

Denton further elaborates
on this model to show how construction of the cell might take less time. However,
even with some advantages in model building the concludes: "Working continually
day and night it would still be difficult to finish the model in the space
of one million years."

Less we forget ... we can
marvel at the complexity and construction of a cell, but there are staggering
issues to comprehend when we move on to an organ such as a mammal's brain!

...
The human brain consists of about ten thousand million nerve cells.
Each nerve cell puts out somewhere in the region of between ten thousand
and one hundred thousand connecting fibers by which it makes contact
with other nerve cells in the brain. All together the total number
of connections in the human brain approaches 1015 or a
thousand million million. Numbers in the order of 1015 are of course completely beyond comprehension.

Despite the enormity
of the number of connections, the ramifying forest of the fibers is
not a chaotic random tangle but a highly organized network in which
a high proportion of the fibers are unique adaptive communication
channels following their own specially ordained pathway through the
brain. Even if only one hundredth of the connections in the brain
and were specifically organized, this would still represent a system
containing a much greater number of specific connections than in the
entire communications network on Earth. Denton
(ETC) Page 330

Denton's quotation
comes from the mid-1980's, so, perhaps it's only fair to say his estimate
for human communication systems is in need of a slight adjustment due to the
more recent advent of the Internet. Lets say two or three hundredths were
specifically organized ... the brain still far exceeds our global
connections.

Earlier in the WindowView
Science Area narrative, there is the strong suggestion that the universe,
chemical origin to life, evolution, and many other perspectives leave us hard
pressed to conclude the cosmos and life within are by chance or random process.
Add to this ... scientists marvel over the architecture and function of the
brain. Science has yet to discover so much about the brain, yet the structure
alone is a clear testimony to design!

Undoubtedly,
the complexity of biological systems in terms of the sheer number of
unique components is very impressive; and it raises the obvious question:
could any sort of purely random process ever have assembled such systems
in the time available? Denton
(ETC) Page 331

Magnifying a cell—to
allow our tour inside—is again a structural experience. The information
housed inside speaks to yet another marvel.

In a separate feature article we illustrate
the incredible nature of DNA to store, replicate, and transport information.
The storage capacity alone for DNA ...

...
is so efficient that all the information needed to specify an organism
as complex as man weighs less than a few thousand millionths of a
gram. The information necessary to specify the design of all the species
of organisms which have ever existed on the planet, a number according
to G. G. Simpson of approximately one thousand million, could be held
in a teaspoon and there would still be room left for all the information
in every book ever written. Denton
(ETC) Page 334

Life is based on the
inner workings of biochemical molecular machines. Embrace the material existence
you live today and leave room to wonder, be awe struck, and consider that
you are the object of what is in fact so remarkable! Life, indeed, is special!

Quotations from "Mere Creation"
(MC) edited by William A. Dembski are used by permission of InterVarsity Press,
P.O. Box 1400, Downers Grove, IL 60515. www.ivpress.com All rights reserved.
No portion of this material may be used without permission from InterVarsity
Press.

Quotations from "Not By
Chance" (NBC) written by L. Spetner, are used by permission granted by
Dr. Lee Spetner.

Writer / Editor: Dr. T. Peterson, Director,
WindowView.org

(090204)

For a general listing of books, visit the WindowView Book Page for: Science and Scripture .

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